Valection: design optimization for validation and verification studies

Authors: Cooper, Christopher, Yao, Delia, Sendorek, Dorota, Yamaguchi, Takafumi, P'ng, Christine, Houlahan, Kathleen, Caloian, Cristian, Fraser, Michael, Ellrott, Kyle, Margolin, Adam, Bristow, Robert, Stuart, Joshua, Boutros, Paul

Source: BMC bioinformatics. 19(1):1-11

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100183813462.0x000001&indx=1&recIds=ETOCvdc_100183813462.0x000001

Germline contamination and leakage in whole genome somatic single nucleotide variant detection

Authors: Sendorek, Dorota, Caloian, Cristian, Ellrott, Kyle, Bare, J., Yamaguchi, Takafumi, Ewing, Adam, Houlahan, Kathleen, Norman, Thea, Margolin, Adam, Stuart, Joshua, Boutros, Paul

Source: BMC bioinformatics. 19(1):1-9

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100161321661.0x000001&indx=1&recIds=ETOCvdc_100161321661.0x000001

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Authors: Lee, Anna, Ewing, Adam, Ellrott, Kyle, Hu, Yin, Houlahan, Kathleen, Bare, J., Espiritu, Shadrielle, Huang, Vincent, Dang, Kristen, Chong, Zechen, Caloian, Cristian, Yamaguchi, Takafumi, Kellen, Michael, Chen, Ken, Norman, Thea, Friend, Stephen, Guinney, Justin, Stolovitzky, Gustavo, Haussler, David, Margolin, Adam, Stuart, Joshua, Boutros, Paul

Source: Genome biology. 19(1):1-15

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185396729.0x000001&indx=1&recIds=ETOCvdc_100185396729.0x000001

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Authors: Allen, Genevera I., Amoroso, Nicola, Anghel, Catalina, Balagurusamy, Venkat, Bare, Christopher J., Beaton, Derek, Bellotti, Roberto, Bennett, David A., Boehme, Kevin L., Boutros, Paul C., Caberlotto, Laura, Caloian, Cristian, Campbell, Frederick, Chaibub Neto, Elias, Chang, Yu-Chuan, Chen, Beibei, Chen, Chien-Yu, Chien, Ting-Ying, Clark, Tim, Das, Sudeshna, Davatzikos, Christos, Deng, Jieyao, Dillenberger, Donna, Dobson, Richard J.B., Dong, Qilin, Doshi, Jimit, Duma, Denise, Errico, Rosangela, Erus, Guray, Everett, Evan, Fardo, David W., Friend, Stephen H., Fröhlich, Holger, Gan, Jessica, St George-Hyslop, Peter, Ghosh, Satrajit S., Glaab, Enrico, Green, Robert C., Guan, Yuanfang, Hong, Ming-Yi, Huang, Chao, Hwang, Jinseub, Ibrahim, Joseph, Inglese, Paolo, Iyappan, Anandhi, Jiang, Qijia, Katsumata, Yuriko, Kauwe, John S.K., Klein, Arno, Kong, Dehan, Krause, Roland, Lalonde, Emilie, Lauria, Mario, Lee, Eunjee, Lin, Xihui, Liu, Zhandong, Livingstone, Julie, Logsdon, Benjamin A., Lovestone, Simon, Ma, Tsung-wei, Malhotra, Ashutosh, Mangravite, Lara M., Maxwell, Taylor J., Merrill, Emily, Nagorski, John, Namasivayam, Aishwarya, Narayan, Manjari, Naz, Mufassra, Newhouse, Stephen J., Norman, Thea C., Nurtdinov, Ramil N., Oyang, Yen-Jen, Pawitan, Yudi, Peng, Shengwen, Peters, Mette A., Piccolo, Stephen R., Praveen, Paurush, Priami, Corrado, Sabelnykova, Veronica Y., Senger, Philipp, Shen, Xia, Simmons, Andrew, Sotiras, Aristeidis, Stolovitzky, Gustavo, Tangaro, Sabina, Tateo, Andrea, Tung, Yi-An, Tustison, Nicholas J., Varol, Erdem, Vradenburg, George, Weiner, Michael W., Xiao, Guanghua, Xie, Lei, Xie, Yang, Xu, Jia, Yang, Hojin, Zhan, Xiaowei, Zhou, Yunyun, Zhu, Fan, Zhu, Hongtu, Zhu, Shanfeng

Source: In Alzheimer's & Dementia: The Journal of the Alzheimer's Association June 2016 12(6):645-653

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

Authors: Zhang, Hongjiu, Wang, Yifan, Guan, Yuanfang, Nguyen, Cu, Sugai, Christopher, Jha, Alokkumar, Li, Jing Woei, Dobin, Alexander, Creason, Allison, Haan, David, Dang, Kristen, Chiotti, Kami E., Inkman, Matthew, Lamb, Andrew, Yu, Thomas, Hu, Yin, Norman, Thea C., Buchanan, Alex, van Baren, Marijke J., Spangler, Ryan, Rollins, M. Rick, Spellman, Paul T., Rozanov, Dmitri, Zhang, Jin, Maher, Christopher A., Caloian, Cristian, Watson, John D., Uhrig, Sebastian, Haas, Brian J., Jain, Miten, Akeson, Mark, Ahsen, Mehmet Eren, Stolovitzky, Gustavo, Guinney, Justin, Boutros, Paul C., Stuart, Joshua M., Ellrott, Kyle

Source: In Cell Systems 18 August 2021 12(8):827-838

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A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

Authors: Creason, Allison, Haan, David, Dang, Kristen, Chiotti, Kami E., Inkman, Matthew, Lamb, Andrew, Yu, Thomas, Hu, Yin, Norman, Thea C., Buchanan, Alex, van Baren, Marijke J., Spangler, Ryan, Rollins, M. Rick, Spellman, Paul T., Rozanov, Dmitri, Zhang, Jin, Maher, Christopher A., Caloian, Cristian, Watson, John D., Uhrig, Sebastian, Haas, Brian J., Jain, Miten, Akeson, Mark, Ahsen, Mehmet Eren, Zhang, Hongjiu, Wang, Yifan, Guan, Yuanfang, Nguyen, Cu, Sugai, Christopher, Jha, Alokkumar, Li, Jing Woei, Dobin, Alexander, Stolovitzky, Gustavo, Guinney, Justin, Boutros, Paul C., Stuart, Joshua M., Ellrott, Kyle

Source: Cell Systems; 20210101, Issue: Preprints